Biology subjects

Silva, M. B.

Publications and source records attributed to Silva, M. B..

4 recordsLinked to original sources

bioRxiv2025

GlomExtractor: a versatile tool for extracting glomerular patches from whole slide kidney biopsy images

The extraction of glomerular image patches is a key step prior to the training and application of glomerular classification models. Numerous algorithms for detecting and segmenting glomeruli have already been described in the literature, but standards for how to extract glomeruli from such an initial annotation remain lacking. Furthermore, the impact of different choices in extracting and preprocessing, such as cropping and scaling, are poorly understood and researched. To address this gap, the current paper introduces the GlomExtractor, a versatile tool implementing the key steps for extracting glomerular patches from whole slide images, including optional filtering of segmentations, patch extraction and scaling, and postprocessing such as background removal. By utilizing the GlomExtractor in combination with glomerular clustering experiments, the current study demonstrated how different processing strategies can impact the performance of downstream machine learning applications. We believe that the GlomExtractor and the experiments demonstrated in the current paper will help researchers in (i) the development of glomerular classification models, in (ii) advancing our understanding of the impact of patch processing on model performance, and in (iii) establishing community standards for how glomeruli should be extracted depending on downstream use.

pathology↗

bioRxiv2024

TRACKING CLONAL AND PLASMID TRANSMISSION IN COLISTIN AND CARBAPENEM RESISTANT KLEBSIELLA PNEUMONIAE

The surveillance of mobile genetic elements facilitating the spread of antimicrobial resistance genes has been challenging. Here, we tracked both clonal and plasmid transmission in colistin- and carbapenem-resistant K. pneumoniae using short and long read sequencing technologies. We observed three clonal transmissions, all containing IncL plasmids and blaNDM-1, although not co-located on the same plasmid. One IncL-blaNDM-1 plasmid had been transferred between ST392 and ST15, and the promiscuous IncL-blaOXA-48 plasmid was likely shared between a singleton and a clonal transmission of ST392. Plasmids within clonal outbreaks and between clusters and STs had 0-2 SNP differences, showing high stability upon transfer to same or different STs. The simplest explanation of a single common IncL-blaNDM-1 plasmid spreading was in fact false, and we found blaNDM-1 in the context of five different plasmids, emphasizing the need to investigate plasmid-mediated transmission for effective containment of outbreaks. IMPORTANCEAntimicrobial resistance occupies a central stage in global public health emergencies. Recently, efforts to track the genetic elements that facilitate the spread of resistance genes to determine so-called plasmid outbreaks have been described, however, such short read sequencing hinders full knowledge about plasmid structure and makes this approach very challenging to implement. In this study we used both short and long read sequencing in clinical Klebsiella pneumoniae from University Hospital Centre Zagreb, Croatia which were resistant to both last resort antibiotics colistin and carbapenem. Our results show complex transmission networks and sharing of plasmids, emphasizing multiple transmissions of plasmids harbouring carbapenem and/or colistin resistance genes between and within K. pneumoniae clones. Only full length sequencing plus a novel way of determining plasmid clusters resulted in the full picture, showing how future active monitoring of plasmids as a vital tool for infection prevention and control could be implemented.

microbiology↗

bioRxiv2022

Factors associated with adherence to annual rabies vaccination in dogs and cats in the municipality of Curuca, Eastern Amazon

Dogs and cats maintain the urban cycle of rabies, and vaccination is the main form of prevention and control of the disease. Brazil has seen human rabies cases transmitted by dogs and cats infected with the bat variant in regions where annual campaigns no longer take place. Although the municipality of Curuca has no cases of urban rabies and viral circulation in wild animals is unknown, there are informal reports of contact of animals and people with vampire bats. This study aimed to identify factors associated with immune response against the rabies virus in dogs and cats in this municipality. A total of 352 dogs and 46 cats were randomly selected for blood collection and their owners answered a questionnaire. The animals were mostly males, aged between 1-3 years, and with unrestricted access to the street. A total of 48.8% of dogs and 32% of cats were not vaccinated in the last anti-rabies campaign, and 4.7% of dogs had been attacked by bats. Among the analyzed samples, only 21.1% had a titration [≥] 0.5 IU/mL. Risk factors for not participating in vaccination campaigns included species, presence of veterinary care, and participation in annual vaccination campaigns (OR = 0.46, 2.55, and 15.67 respectively). The animal population was estimated at 18,620 dogs and 4,556 cats. The human:dog ratio was 2.1:1 and the human:cat ratio was 8.7:1. This study revealed that the estimated population of dogs based on the human population was an underestimate for communities in the Amazon region. This was the first time that the number of dogs attacked by bats was determined. Health education with an emphasis on responsible ownership and periodic and biannual rabies vaccinations are recommended for the municipality. AUTHOR SUMMARYRabies is a viral disease characterized by brain and spinal cord inflammation. It affects all mammals, being almost 100% lethal. Hematophagous bats are one of the main wild reservoirs responsible for outbreaks of human rabies in the state of Para and other regions of Brazil. Vaccination is the most effective form of control and prevention, even where rabies is believed to be under control. The levels of antibodies that fight the rabies virus must be constantly monitored through serological analysis to assess the effectiveness of vaccination programs. In the municipality of Curuca, Para, bats commonly attack people and their pets, and anti-rabies campaigns are not promoted every year. In the present study, we determined the number of attacks by bats on domestic dogs and estimated vaccination coverage and the canine and feline population in the municipality, which was underestimated. This information can be useful for future vaccination campaigns. The study identified factors associated with responsible ownership that interfere with the protective titration of animals against rabies and suggests promoting more than one annual anti-rabies campaign in this location.

scientific communication and education↗

bioRxiv2019

Crab fisherman communities in north Brazil: a new high risk population for vampire bat rabies

An outbreak of human rabies transmitted by hematophagous bats occurred in 2018 in the state of Para, Brazil, eastern Amazon, after 14 years with no record of the disease. It is necessary to understand the epidemiological characteristics of these attacks to protect the local population. This study aimed to characterize attacks of humans by vampire bats in the municipality of Sao Joao da Ponta, Para state, Brazil, from 2013 to 2015. All individuals attacked by bats who sought medical care during the study period (n=5) were identified in the Notifiable Diseases Information System (SINAN) database and answered a questionnaire about the circumstances of the attack. Using snowball sampling, seed cases identified other individuals who were attacked in the same period but did not seek medical care (n=61), totalizing 66 people attacked in the same period. The interviewees were male (92.4%), adults between 20 and 50 years old (69.6%) and had completed elementary education (86.3%). Most were rural residents (92.4%) and crab fishermen (79.3%). The interviewees (92.4%) identified the mangrove of the Mae Grande de Curuca extractive reserve as an area conducive to attacks by vampire bats, where groups of fishermen sometimes concentrate for days for crab fishing, often living in improvised dwellings without walls and covered by tarps or straw (88.8%). The wounds were single bites (71.2%) and were located on the lower limbs (93.9%). Overall, 42.4% of participants had been bitten more than four times throughout their life (range 1-23 attacks). Participants were unaware of the risk of contracting rabies by the bite (95.4%). Using Sao Joao da Ponta as a model, this study shows that bat attacks are an essentially occupational problem in the study region. Indeed, for each reported attack, there are 12.2 unreported cases. It is necessary to develop strategies to reach this population for prophylactic treatment.\n\nAuthor SummaryDifferent from which occurs worldwide in relation to rabies transmission, in Amazon region, vampire bat is involved on direct transmission of rabies virus to humans when searching for bloodmeal. It is common in the state of Para, Eastern Amazon, large areas inhabited near forests and mangroves. People living there use forest natural resources as a way of income and sustenance and these working conditions is what our study points out as an important factor for aggressions predisposition. Here this subject is shown as an occupational problem. This study also quantified for the first time underreported humans aggressions by bats in Amazon, using the snowball sampling, which valued the relationship between individuals to reach the target population. Based on these results, rabies surveillance may direct actions for prevention and health education for these individuals, including changes in notifications forms and suggesting pre-exposure prophylaxis in vaccination calendar of the Brazilian Ministry of Health for these individuals exposed to the rabies virus.

epidemiology↗